Is CTRC p.Ser16= (c.48C>T) pathogenic?

CTRC p.Ser16= (c.48C>T) is classified Likely benign in CTRC (ClinVar, Single submitter, 1 submitter; last evaluated 2021-05-13). No allele count reported in gnomAD v4.1 (AN 1,607,228); Associated with hereditary chronic pancreatitis.

What condition is associated with CTRC p.Ser16= (c.48C>T)?

CTRC p.Ser16= (c.48C>T) is associated with hereditary chronic pancreatitis (ClinVar).

How common is CTRC p.Ser16= (c.48C>T) in the general population?

CTRC p.Ser16= (c.48C>T) is no allele count reported in gnomAD v4.1 (AN 1,607,228) (gnomAD).

CTRC p.Ser16=

Q: How is Autosomal dominant hereditary chronic pancreatitis inherited?

Typically Autosomal dominant (Orphanet). A genetic counselor can assess individual risk for a family.

c.48C>T · rs753438186 · VCV1743942

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,607,228)

Conditions

hereditary chronic pancreatitis

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 2.6	GERP 2.2, phastCons 1
Overall
CADD	9.927	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,607,228). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: CTRC
Protein: p.Ser16=
Coding: c.48C>T
MANE Select: NM_007272
dbSNP: rs753438186
Type: single nucleotide variant
Location: chr1:15440307 (GRCh38)
Gene constraint: LOEUF 1.147 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 94.03 · 1 PDB

Full CTRC gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

hereditary chronic pancreatitis — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Autosomal dominant hereditary chronic pancreatitis (Orphanet):

Inheritance: Autosomal dominant
Onset: Adolescent, Childhood
Prevalence: 1-9 / 1 000 000 (France)

Similar variants

CTRC p.Ser16Ile Uncertain significance ★★ ⚠ same residue
CTRC p.Ser16Arg Uncertain significance ★ same residue
CTRC p.Ser16Asn Uncertain significance ★ ⚠ same residue
CTRC p.Ser16Gly Conflicting classifications of pathogenicity ★ ⚠ same residue
CTRC c.494-1G>C Pathogenic/Likely pathogenic ★★ same condition
CTRC p.Arg29Ter Pathogenic/Likely pathogenic ★★ same condition
CTRC p.Gln174Ter Pathogenic/Likely pathogenic ★★ same condition
CTRC c.356+1G>A Uncertain significance ★★ same condition

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/ctrc-p-ser16 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown